Denis Dupuy et al. (2007) International Worm Meeting "Genome-scale analysis of in vivo spatiotemporal promoter activity in C. elegans."

Rock Pulak, David Baillie, David Lee, Kavitha Venkatesan, Denis Dupuy, William Mohler, Ian Hope, Marc Vidal, Cesar Hidalgo, Donald Moerman, Ryan Viveiros, Nenad Svrzikapa, Murat Tasan, Albert-Laszlo Barabasi, Anne-Ruxandra Carvunis, John Reece-Hoyes, Frederick Roth, Domena Tu, Rebecca Hunt-Newbury, Nicolas Bertin

[International Worm Meeting, 2007]

*The first 3 authors contributed equally. Correspondence should be addressed to any of the last 3 authors. Much of the complexity of metazoan organisms comes from differential expression of genes to drive cell differentiation. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step towards understanding complex biological systems. We developed a new application that enables high-throughput fluorescence expression pattern acquisition, using the nematode profiler (COPAS, Union Biometrica). Individual profiles collected from a mixed stage population are arranged by size into post-embryonic expression chronograms. A chronogram provides a reconstituted time-lapse image of gene expression during development from larva to adult across the length of the worm body. This data format allows unsupervised comparison and clustering of expression patterns, while also providing a clear temporal overview of gene expression. We present an analysis of the spatiotemporal activity of ~5% of the predicted C. elegans promoters driving the expression of green fluorescent protein (GFP) in vivo. Automated comparison and clustering of the obtained ~900 chronograms show that genes co-expressed in space and time tend to belong to common functional categories. Moreover, integration of this localizome dataset with C. elegans protein interactome datasets enables prediction of interaction territories between protein partners.